RetrogeneDB ID: retro_fcat_1606

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:89777744..89778505(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000025551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSFCAG00000029191
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_fcat_1606
GGGCTGGGCCAGGACCACGGAACTCACAGAGGAAACACCAAGGACAAGGAGTGGATCTCCATCAACAAGCTGAGCCAACT
GGTCGACATCATGAAGATCAAGGCCCTGAAAGAGCTCTCTCTCTCCTCCCTGCCCATCAAGGAATCTGAGATCATTGACT
TTTTCCTGGACACATCCCAGGAAGTGATGAGGTTTGAAGTTTTGAAAATTATGCCTGTGCAGAAGCAGACCCAGGCTGGC
CAGAGGACCAGGTGCAAGGCATTTGTTGCCATTGGAGAGCACAAAGGACACGTAGGTCTGGGTGTTAAGTTCTCTAAGGA
GGTAGCCACTGCCTTCCATGAGGCCATCGTCCTGCACAAGCCTTTCCACCGTCTCATGTGGCGAAGCTACTGGGGGAACC
AGCTCGGCGAGGCCCACACTATCCCATGCAAGGGGACCAGACACTGTGACTCTGTGCTGGACGCCTCATCCCCTACACCA
GGGGCAGGGGCATTCTCTCGGCCCCCGTGCCCAAGACGATACTGATGATGGCAGGCATTGACGACTGCTACCTCTCCACC
AGGGGCTACGCTGCCACCCTGGGCCACTTCACCAAGGCCACTTTTGATGCTATTCCCAAGACCTACAGCTACCGTGCCCC
TGACCTCTGGAAAGAGACGGTATTCACCAAGTCTCCCCGTCAGGAATTCACTGACCAGCTTGCAAAGACCCACACCAGAG
TCTCTGTGCAGAAGACCCAGGCTCCAGCTGTGGCCACCACA

Alignment

ORF - retro_fcat_1606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 85.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGARGGKAEDKEWMPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGAS---LKDEVLKI
          G.G...G...G...DKEW....KL..LV..MKIK.L.E..L.SLPIKESEIIDFFL..S......EVLKI
Retrocopy GLGQDHGTHRGNTKDKEWISINKLSQLVDIMKIKALKELSLSSLPIKESEIIDFFLDTSQEVMRFEVLKI

Parental  MPVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHT
          MPVQKQT.AGQRTR.KAFVAIG...GHVGLGVK.SKEVATA...AI.L.K.......R.YWGN..G..HT
Retrocopy MPVQKQTQAGQRTRCKAFVAIGEHKGHVGLGVKFSKEVATAFHEAIVLHKPFHRLMWRSYWGNQLGEAHT

Parental  VPCKVTGRCGSVLV-RLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTY
          .PCK.T..C.SVL..RLIP..RG.GI.SAPVPK..LMMAGIDDCY.S.RG..ATLG.F.KATFDAI.KTY
Retrocopy IPCKGTRHCDSVLD<RLIPYTRGRGILSAPVPKTILMMAGIDDCYLSTRGYAATLGHFTKATFDAIPKTY

Parental  SYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
          SY..PDLWKETVFTKSP.QEFTD.L.KTHTRVSVQ.TQAPAVATT
Retrocopy SYRAPDLWKETVFTKSPRQEFTDQLAKTHTRVSVQKTQAPAVATT

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	283.83 RPM
SRP017611_kidney	0.00 RPM	608.66 RPM
SRP017611_liver	0.00 RPM	446.62 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1606 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1606 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 12 parental genes, and 211 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Callithrix jacchus	ENSCJAG00000015267	15 retrocopies	retro_cjac_1482, retro_cjac_1585, retro_cjac_1609, retro_cjac_1712, retro_cjac_1964, retro_cjac_2201, retro_cjac_2255, retro_cjac_2284, retro_cjac_2361, retro_cjac_2493, retro_cjac_2620, retro_cjac_274, retro_cjac_317, retro_cjac_3741, retro_cjac_4194,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606 , retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens	ENSG00000140988	47 retrocopies	retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688, retro_hsap_1722, retro_hsap_1812, retro_hsap_1830, retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Gorilla gorilla	ENSGGOG00000009371	5 retrocopies	retro_ggor_129, retro_ggor_1391, retro_ggor_1428, retro_ggor_168, retro_ggor_390,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Microcebus murinus	ENSMICG00000012765	28 retrocopies	retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Otolemur garnettii	ENSOGAG00000010098	19 retrocopies	retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri	ENSTBEG00000006726	30 retrocopies	retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,
Tarsius syrichta	ENSTSYG00000013466	52 retrocopies	retro_tsyr_1069, retro_tsyr_1078, retro_tsyr_1147, retro_tsyr_1301, retro_tsyr_131, retro_tsyr_1317, retro_tsyr_1466, retro_tsyr_1478, retro_tsyr_1498, retro_tsyr_1505, retro_tsyr_1509, retro_tsyr_1536, retro_tsyr_1564, retro_tsyr_1568, retro_tsyr_1588, retro_tsyr_1614, retro_tsyr_1636, retro_tsyr_1658, retro_tsyr_169, retro_tsyr_1789, retro_tsyr_1804, retro_tsyr_1827, retro_tsyr_186, retro_tsyr_1929, retro_tsyr_1935, retro_tsyr_2016, retro_tsyr_2175, retro_tsyr_290, retro_tsyr_349, retro_tsyr_415, retro_tsyr_417, retro_tsyr_463, retro_tsyr_472, retro_tsyr_525, retro_tsyr_527, retro_tsyr_545, retro_tsyr_568, retro_tsyr_604, retro_tsyr_605, retro_tsyr_609, retro_tsyr_61, retro_tsyr_622, retro_tsyr_638, retro_tsyr_650, retro_tsyr_672, retro_tsyr_689, retro_tsyr_691, retro_tsyr_699, retro_tsyr_768, retro_tsyr_773, retro_tsyr_922, retro_tsyr_980,