RetrogeneDB ID: retro_ecab_1105

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:38172227..38172979(-)
• Located in intron of: ENSECAG00000012700

Retrocopy information

• Ensembl ID: ENSECAG00000016634
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSECAG00000009065
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_ecab_1105
GGCCGGGGTCACGGCCGCAGAGCTCGCGGAGCAAGGCCGAGGACAAGGAGTGGATCCCCGTCACCAAGCTGGGTCACCTG
GTCAAAGACATGAAGATCAAGTCCCTGGAGGAATCTACCTTTTCTCCCTGCCCATCAAGGAGTCTGAGATCATTGACTCT
TTCCTGGGGGCATCTCTCAAGGAGGAGGTTTTGAAGATTATGCCGGTGCAAAAGCACACCCGTGCTGGCCAGCGGACCAG
GTTCAAGGCATTTGTTGCCATCGGGGATTACAATGGACATGTCGGTCTGGGTGTGAAGTGCTCCAAGGAGGTAGCCACTG
CCATCCGTGGGGGCATCATCCTTGCCAAACTCTCCATTATTCCCGTGCGACGAGGCTACTGGGGGAACAAGATCGGCAAG
CCCCCATACTGCTCCTTACAAGGTGACAGGTCGCTGTGGCTCTGTGCTGGTGTGCCTCATCCCTGCCCCCAGGGGCAGTG
GCATTGTGTCAGCCCCTGTGCCCAAGAAGCTCTTGATGATGGCTGGTATTGACAACTGCTACACCTCAGCCAGGGGCTGT
ACTGCCACCCTTGGCAACTTTGCCAAGGCCACCTTTGATGCCATCTCTAAGACCTACAGCTATCTCACCCCCGACCCCTG
GAAAGAGACCGTGTTCACCAAGTCTCCCTATCAGGAGTTCACTGACCATCTTGTAAAGAACCACACCAGAGTCTCCGTGC
AGAGGACCCAGGCTCCAGCTGTGGCTACCACA

Alignment

ORF - retro_ecab_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.91 %
• Parental protein coverage: 85.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GRGRGRGARGG-KAEDKEWIPVTKLGRLVKDMKIKSLEE-IYLFSLPIKESEIIDFFLGASLKDEVLKIM
          GRG.GR.ARG..KAEDKEWIPVTKLG.LVKDMKIKSLEE.IYLFSLPIKESEIID.FLGASLK.EVLKIM
Retrocopy GRGHGRRARGA<KAEDKEWIPVTKLGHLVKDMKIKSLEE<IYLFSLPIKESEIIDSFLGASLKEEVLKIM

Parental  PVQKQTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKP-HT
          PVQK.TRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRG.IILAKLSI.PVRRGYWGNKIGKP.HT
Retrocopy PVQKHTRAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGGIILAKLSIIPVRRGYWGNKIGKP>HT

Parental  VPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYS
          .P.KVTGRCGSVLV.LIPAPRG.GIVSAPVPKKLLMMAGID.CYTSARGCTATLGNFAKATFDAISKTYS
Retrocopy APYKVTGRCGSVLVCLIPAPRGSGIVSAPVPKKLLMMAGIDNCYTSARGCTATLGNFAKATFDAISKTYS

Parental  YLTPDLWKETVFTKSPYQEFTDHLVKNHTRVSVQRTQAPAVATT
          YLTPD.WKETVFTKSPYQEFTDHLVKNHTRVSVQRTQAPAVATT
Retrocopy YLTPDPWKETVFTKSPYQEFTDHLVKNHTRVSVQRTQAPAVATT

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
SRP021940_articular_cartilage	0.83 RPM	1345.23 RPM
SRP021940_cerebellum	0.26 RPM	357.55 RPM
SRP021940_embryo	1.20 RPM	851.49 RPM
SRP021940_placental_villous	0.87 RPM	688.28 RPM
SRP021940_synovial_membrane	0.99 RPM	1087.71 RPM
SRP021940_testis	0.77 RPM	354.05 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1105 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1105 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105 , retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,