RetrogeneDB ID: retro_fcat_139

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:99563056..99563578(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000024634
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FTL
• Ensembl ID: ENSFCAG00000003348
• Aliases: None
• Description: Ferritin light chain [Source:UniProtKB/Swiss-Prot;Acc:Q2MHN1]

Sequence

>retro_fcat_139
ATGAGCTGCCAGATTAATCAGAATTATTCCACTAAGTTGGAGACTGCCACCAATTGCCTGGTCAACATGCATCTGCGGGC
CTCCTACACCTTCCTCTCTCTGGGCTTCTATTTCAACCGTGAGGATGTGGCTCTGGAGGGTGTGAGCCACTTCTACAAGT
TGGCTGAGGAGAAGCGCAAGGGTGCTGAGCATCTCTTGAAGATGCAAAACCAGTGTGGTGGCCACACTCTCTCCCAGGAT
ATGCAGAAGCCATCCCAAGATGAGTGGGGTAAAACTCAGGATGCCCTGGAAGCTGCCCTATTTCTGGAGAAGAACCTGAA
CCAGGCCCTTTTGAATCTGCATGCCTTGGGTTCTGCCCATGCAGACATGCATCTCTGTGACTTCCTGGAGAACCACTTCC
TAGATGAGGAGGTGCAGCTCATCGAGAAGATGCTCAACCTTCTGACTAACCTCCGCAGGCTGGCTGGCTCCCAGGCTGGG
CTGGGTGAGTATCTCTTCGAAAGGCTCACCCTCAACCACAAC

Alignment

ORF - retro_fcat_139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSQIRQNYSTEVEAAVNRLVNMHLRASYTYLSLGFYFDRDDVALEGVGHFFRELAEEKREGAERLLKMQ
          MS.QI.QNYST..E.A.N.LVNMHLRASYT.LSLGFYF.R.DVALEGV.HF...LAEEKR.GAE.LLKMQ
Retrocopy MSCQINQNYSTKLETATNCLVNMHLRASYTFLSLGFYFNREDVALEGVSHFYK-LAEEKRKGAEHLLKMQ

Parental  NQRGGRALFLDVQKPSQDEWGKTLDAMEAALLLEKNLNQGLLDLHALGSARADPHLCDFLENHFLDEEVK
          NQ.GG..L..D.QKPSQDEWGKT.DA.EAAL.LEKNLNQ.LL.LHALGSA.AD.HLCDFLENHFLDEEV.
Retrocopy NQCGGHTLSQDMQKPSQDEWGKTQDALEAALFLEKNLNQALLNLHALGSAHADMHLCDFLENHFLDEEVQ

Parental  LIKKMGDHLTNLRRLSGPQAELGEYLFERLTLKHD
          LI.KM...LTNLRRL.G.QA.LGEYLFERLTL.H.
Retrocopy LIEKMLNLLTNLRRLAGSQAGLGEYLFERLTLNHN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	75.41 RPM
SRP017611_kidney	0.00 RPM	1819.59 RPM
SRP017611_liver	0.00 RPM	1019.39 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_139 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_139 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 35 parental genes, and 531 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014582	27 retrocopies	retro_amel_1008, retro_amel_1182, retro_amel_1185, retro_amel_1218, retro_amel_1277, retro_amel_1342, retro_amel_1419, retro_amel_1549, retro_amel_1638, retro_amel_1642, retro_amel_1753, retro_amel_178, retro_amel_1784, retro_amel_1872, retro_amel_1925, retro_amel_202, retro_amel_220, retro_amel_250, retro_amel_348, retro_amel_52, retro_amel_580, retro_amel_614, retro_amel_624, retro_amel_650, retro_amel_698, retro_amel_861, retro_amel_907,
Bos taurus	ENSBTAG00000013343	33 retrocopies	retro_btau_1007, retro_btau_1011, retro_btau_1033, retro_btau_1197, retro_btau_1209, retro_btau_1277, retro_btau_1354, retro_btau_1396, retro_btau_1452, retro_btau_1464, retro_btau_1466, retro_btau_1481, retro_btau_1511, retro_btau_1540, retro_btau_1561, retro_btau_1683, retro_btau_1781, retro_btau_1798, retro_btau_1848, retro_btau_250, retro_btau_301, retro_btau_339, retro_btau_340, retro_btau_419, retro_btau_422, retro_btau_520, retro_btau_597, retro_btau_639, retro_btau_649, retro_btau_938, retro_btau_963, retro_btau_993, retro_btau_998,
Canis familiaris	ENSCAFG00000003861	1 retrocopy	retro_cfam_203,
Callithrix jacchus	ENSCJAG00000000250	13 retrocopies	retro_cjac_1171, retro_cjac_1208, retro_cjac_1264, retro_cjac_1643, retro_cjac_2272, retro_cjac_2780, retro_cjac_3113, retro_cjac_3254, retro_cjac_3879, retro_cjac_556, retro_cjac_60, retro_cjac_889, retro_cjac_997,
Cavia porcellus	ENSCPOG00000020558	1 retrocopy	retro_cpor_100,
Dasypus novemcinctus	ENSDNOG00000002455	9 retrocopies	retro_dnov_1096, retro_dnov_1135, retro_dnov_1177, retro_dnov_1737, retro_dnov_2006, retro_dnov_2352, retro_dnov_2678, retro_dnov_473, retro_dnov_993,
Dasypus novemcinctus	ENSDNOG00000004126	5 retrocopies	retro_dnov_1263, retro_dnov_1490, retro_dnov_1760, retro_dnov_2329, retro_dnov_299,
Dasypus novemcinctus	ENSDNOG00000005577	36 retrocopies	retro_dnov_103, retro_dnov_1164, retro_dnov_1215, retro_dnov_130, retro_dnov_1382, retro_dnov_1441, retro_dnov_1515, retro_dnov_1568, retro_dnov_1657, retro_dnov_1812, retro_dnov_1815, retro_dnov_1918, retro_dnov_1991, retro_dnov_2014, retro_dnov_2134, retro_dnov_2187, retro_dnov_236, retro_dnov_2376, retro_dnov_2379, retro_dnov_247, retro_dnov_2575, retro_dnov_2658, retro_dnov_2667, retro_dnov_285, retro_dnov_305, retro_dnov_432, retro_dnov_439, retro_dnov_543, retro_dnov_598, retro_dnov_642, retro_dnov_807, retro_dnov_841, retro_dnov_846, retro_dnov_849, retro_dnov_861, retro_dnov_897,
Dasypus novemcinctus	ENSDNOG00000007848	2 retrocopies	retro_dnov_1049, retro_dnov_1476,
Dasypus novemcinctus	ENSDNOG00000016683	8 retrocopies	retro_dnov_1134, retro_dnov_1329, retro_dnov_2023, retro_dnov_2194, retro_dnov_2228, retro_dnov_56, retro_dnov_757, retro_dnov_886,
Dipodomys ordii	ENSDORG00000015550	5 retrocopies	retro_dord_222, retro_dord_34, retro_dord_618, retro_dord_776, retro_dord_79,
Felis catus	ENSFCAG00000003348	37 retrocopies	retro_fcat_101, retro_fcat_1029, retro_fcat_1040, retro_fcat_1059, retro_fcat_1141, retro_fcat_1150, retro_fcat_1295, retro_fcat_1319, retro_fcat_1336, retro_fcat_1359, retro_fcat_139 , retro_fcat_1522, retro_fcat_1523, retro_fcat_1602, retro_fcat_1658, retro_fcat_1741, retro_fcat_1747, retro_fcat_1764, retro_fcat_1765, retro_fcat_1766, retro_fcat_1799, retro_fcat_1812, retro_fcat_1901, retro_fcat_297, retro_fcat_298, retro_fcat_315, retro_fcat_343, retro_fcat_50, retro_fcat_533, retro_fcat_536, retro_fcat_620, retro_fcat_675, retro_fcat_68, retro_fcat_778, retro_fcat_918, retro_fcat_927, retro_fcat_964,
Felis catus	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
Homo sapiens	ENSG00000087086	11 retrocopies	retro_hsap_1647, retro_hsap_1955, retro_hsap_2407, retro_hsap_2484, retro_hsap_2942, retro_hsap_3842, retro_hsap_4146, retro_hsap_431, retro_hsap_4665, retro_hsap_4805, retro_hsap_929,
Gorilla gorilla	ENSGGOG00000011999	9 retrocopies	retro_ggor_128, retro_ggor_1547, retro_ggor_2039, retro_ggor_25, retro_ggor_2784, retro_ggor_2894, retro_ggor_420, retro_ggor_677, retro_ggor_750,
Loxodonta africana	ENSLAFG00000031248	11 retrocopies	retro_lafr_1003, retro_lafr_1064, retro_lafr_1065, retro_lafr_1069, retro_lafr_1206, retro_lafr_255, retro_lafr_345, retro_lafr_346, retro_lafr_785, retro_lafr_836, retro_lafr_977,
Microcebus murinus	ENSMICG00000001861	7 retrocopies	retro_mmur_1017, retro_mmur_1238, retro_mmur_1420, retro_mmur_1506, retro_mmur_204, retro_mmur_214, retro_mmur_681,
Macaca mulatta	ENSMMUG00000003909	9 retrocopies	retro_mmul_1051, retro_mmul_1125, retro_mmul_1508, retro_mmul_1569, retro_mmul_1617, retro_mmul_1950, retro_mmul_481, retro_mmul_518, retro_mmul_989,
Mustela putorius furo	ENSMPUG00000003304	29 retrocopies	retro_mputfur_1012, retro_mputfur_1026, retro_mputfur_1133, retro_mputfur_1142, retro_mputfur_1150, retro_mputfur_1216, retro_mputfur_1222, retro_mputfur_1225, retro_mputfur_1238, retro_mputfur_1246, retro_mputfur_1268, retro_mputfur_1303, retro_mputfur_1335, retro_mputfur_1521, retro_mputfur_1620, retro_mputfur_195, retro_mputfur_222, retro_mputfur_265, retro_mputfur_350, retro_mputfur_356, retro_mputfur_368, retro_mputfur_482, retro_mputfur_66, retro_mputfur_702, retro_mputfur_741, retro_mputfur_80, retro_mputfur_820, retro_mputfur_906,