RetrogeneDB ID: retro_acar_173

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343304.1:613245..613587(-)
• Located in intron of: ENSACAG00000011262

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSACAG00000005311
• Aliases: None
• Description: None

Sequence

>retro_acar_173
ACTTCCCACACTTTCTGGAGGTCCAAAACCCTACGGTTATGGTAGCCGCCCAAATACCCCTGGAAGAGTGCACCCAGGAG
GAACAAGTTGGACCATTATGCCATCATCAAGTTCCCTCTGACAACTGAGTTGGCCATGAAGAAGATCAAGGACAACACCT
TGGTCTTCATTGTGGACATCAAGGCCAATAAGCACCAGATCAAGCAGGCTGTCAAGAAGTTGTATGACATTGACGTGGCA
AAAGTCAATACACTTATCAGTCCTGATGGCAAAAAGAAGGCCTACATTCATTTTGCTCCGGATTATGACGCTCTAGATGT
AGCCAAGAAGATTAGTATCATC

Alignment

ORF - retro_acar_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.35 %
• Parental protein coverage: 74.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQ
          TS.TF.R.KTLRL...PKYP.KSAPRRNKLDHYAIIKFPLTTE.AMKKI.DN.TLVFIVD.KANKHQIKQ
Retrocopy TSHTFWRSKTLRLW*PPKYPWKSAPRRNKLDHYAIIKFPLTTELAMKKIKDN-TLVFIVDIKANKHQIKQ

Parental  AVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII
          AVKKLYDIDVAKVNTLI.PDG.KKAY...APDYDALDVA.KI.II
Retrocopy AVKKLYDIDVAKVNTLISPDGKKKAYIHFAPDYDALDVAKKISII

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
SRP009831_adrenal	0.00 RPM	1239.00 RPM
SRP009831_brain	0.00 RPM	266.43 RPM
SRP009831_dewlap	0.00 RPM	446.38 RPM
SRP009831_embryo	0.06 RPM	672.26 RPM
SRP009831_heart	0.00 RPM	476.33 RPM
SRP009831_liver	0.00 RPM	628.13 RPM
SRP009831_lung	0.00 RPM	454.06 RPM
SRP009831_ovary	0.00 RPM	308.06 RPM
SRP009831_skeletal_muscle	0.00 RPM	263.18 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_173 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_173 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis 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 19 parental genes, and 261 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005311	2 retrocopies	retro_acar_152, retro_acar_173 ,
Ailuropoda melanoleuca	ENSAMEG00000004684	31 retrocopies	retro_amel_1044, retro_amel_1154, retro_amel_121, retro_amel_1254, retro_amel_1302, retro_amel_1383, retro_amel_1391, retro_amel_1423, retro_amel_1503, retro_amel_1505, retro_amel_1511, retro_amel_1527, retro_amel_1532, retro_amel_1568, retro_amel_1576, retro_amel_1585, retro_amel_1702, retro_amel_1822, retro_amel_288, retro_amel_304, retro_amel_323, retro_amel_467, retro_amel_479, retro_amel_514, retro_amel_667, retro_amel_75, retro_amel_773, retro_amel_843, retro_amel_894, retro_amel_901, retro_amel_956,
Bos taurus	ENSBTAG00000046394	6 retrocopies	retro_btau_132, retro_btau_159, retro_btau_169, retro_btau_178, retro_btau_237, retro_btau_8,
Callithrix jacchus	ENSCJAG00000013126	7 retrocopies	retro_cjac_118, retro_cjac_154, retro_cjac_20, retro_cjac_258, retro_cjac_30, retro_cjac_315, retro_cjac_46,
Cavia porcellus	ENSCPOG00000001452	6 retrocopies	retro_cpor_1275, retro_cpor_1304, retro_cpor_1311, retro_cpor_153, retro_cpor_445, retro_cpor_966,
Equus caballus	ENSECAG00000008928	1 retrocopy	retro_ecab_42,
Felis catus	ENSFCAG00000004021	35 retrocopies	retro_fcat_1003, retro_fcat_1011, retro_fcat_1030, retro_fcat_1039, retro_fcat_1054, retro_fcat_1071, retro_fcat_1073, retro_fcat_11, retro_fcat_1124, retro_fcat_1161, retro_fcat_1202, retro_fcat_1205, retro_fcat_1275, retro_fcat_1389, retro_fcat_1659, retro_fcat_1670, retro_fcat_1748, retro_fcat_1787, retro_fcat_1796, retro_fcat_1810, retro_fcat_182, retro_fcat_185, retro_fcat_1856, retro_fcat_1905, retro_fcat_1909, retro_fcat_1944, retro_fcat_2022, retro_fcat_289, retro_fcat_364, retro_fcat_476, retro_fcat_603, retro_fcat_657, retro_fcat_765, retro_fcat_898, retro_fcat_950,
Gorilla gorilla	ENSGGOG00000016736	26 retrocopies	retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana	ENSLAFG00000013387	16 retrocopies	retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Myotis lucifugus	ENSMLUG00000012448	4 retrocopies	retro_mluc_175, retro_mluc_2375, retro_mluc_353, retro_mluc_91,
Monodelphis domestica	ENSMODG00000019297	3 retrocopies	retro_mdom_120, retro_mdom_870, retro_mdom_912,
Mustela putorius furo	ENSMPUG00000014179	12 retrocopies	retro_mputfur_102, retro_mputfur_106, retro_mputfur_123, retro_mputfur_159, retro_mputfur_168, retro_mputfur_179, retro_mputfur_3, retro_mputfur_333, retro_mputfur_42, retro_mputfur_52, retro_mputfur_599, retro_mputfur_91,
Mus musculus	ENSMUSG00000058546	8 retrocopies	retro_mmus_1, retro_mmus_126, retro_mmus_130, retro_mmus_184, retro_mmus_224, retro_mmus_64, retro_mmus_84, retro_mmus_95,
Pongo abelii	ENSPPYG00000008108	49 retrocopies	retro_pabe_1030, retro_pabe_1203, retro_pabe_1206, retro_pabe_1335, retro_pabe_1430, retro_pabe_1459, retro_pabe_1590, retro_pabe_1721, retro_pabe_1747, retro_pabe_1752, retro_pabe_1766, retro_pabe_1797, retro_pabe_1846, retro_pabe_1848, retro_pabe_1867, retro_pabe_1926, retro_pabe_1947, retro_pabe_1995, retro_pabe_2018, retro_pabe_2057, retro_pabe_2075, retro_pabe_2082, retro_pabe_2091, retro_pabe_2132, retro_pabe_2156, retro_pabe_2221, retro_pabe_2334, retro_pabe_234, retro_pabe_243, retro_pabe_2612, retro_pabe_2738, retro_pabe_2773, retro_pabe_2820, retro_pabe_2944, retro_pabe_3006, retro_pabe_3036, retro_pabe_3200, retro_pabe_3371, retro_pabe_3477, retro_pabe_351, retro_pabe_3528, retro_pabe_354, retro_pabe_474, retro_pabe_627, retro_pabe_754, retro_pabe_765, retro_pabe_799, retro_pabe_946, retro_pabe_984,
Rattus norvegicus	ENSRNOG00000023344	6 retrocopies	retro_rnor_136, retro_rnor_145, retro_rnor_211, retro_rnor_40, retro_rnor_404, retro_rnor_62,
Sarcophilus harrisii	ENSSHAG00000014549	13 retrocopies	retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,
Sus scrofa	ENSSSCG00000017768	9 retrocopies	retro_sscr_1025, retro_sscr_1047, retro_sscr_1133, retro_sscr_239, retro_sscr_356, retro_sscr_418, retro_sscr_598, retro_sscr_638, retro_sscr_952,
Sus scrofa	ENSSSCG00000029802	4 retrocopies	retro_sscr_115, retro_sscr_170, retro_sscr_248, retro_sscr_430,
Ictidomys tridecemlineatus	ENSSTOG00000011328	23 retrocopies	retro_itri_1022, retro_itri_1035, retro_itri_1051, retro_itri_1059, retro_itri_1071, retro_itri_1150, retro_itri_1261, retro_itri_1327, retro_itri_1347, retro_itri_1460, retro_itri_1507, retro_itri_217, retro_itri_225, retro_itri_304, retro_itri_360, retro_itri_494, retro_itri_626, retro_itri_627, retro_itri_734, retro_itri_761, retro_itri_791, retro_itri_965, retro_itri_972,