RetrogeneDB ID: retro_ecab_361

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 16:45791698..45792853(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000012893
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSECAG00000021928
• Aliases: None
• Description: RAD23 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:9813]

Sequence

>retro_ecab_361
GTGAAAGCACTGGAGGAGAAGATCGAGTCTGAAAAGGGGAAAGATGCCTTTCCTGTAGCAGGTCAAAAATTAATTTATGC
AGGCAAAATCCTCAATGATGATACTGCTCTAAAGGAATATAAAATTGATGAGAAAAACTTTGTGGTGGTTATGGTGACAA
AACCCAAAGCAGTGACAACACCAGCACCAGCTACAACACAGCAATCAAATTCTGCCACCACTACCACATAGTTCCTCCAC
AGCACCAGCTGTGGCTCAGGCTCCAACCCCCGCCCCTGCCTTGGCTCCCACTCCCACCCCTGCATCCATCACTCCAGCAT
CAGCAACAGCATCTTCTGAACCTGCACCTGCTAGTGCAACGAAACAAGAGAAACCTGCAGAAAAGCCAGCAGAAACACCA
GTGGCTACTAGCCCAACATCAACTGACTGTACATCAGGAGATTCTTCTCGGTCAAACCTTTTTGAAGATGCAACAAGTGC
GCTTGTGACAGGTCAGTCTTATGAGAATATGGTAGCAGAGATCATGTCAATGGGCTGTGAACGAGAGCAAGTAATTGCGG
CCCTGAGAGCCAGTTTCAACAACCCTGACAGAGCAGTGGAGTATCTTTTCATGGGAATCCCTGGAGACAGAGAGAGTCAG
GCTGTGGTTGACCCCCCTCCAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAGTGGCTGCAGCTGCAGCAACCACGACAGC
GACGACTACAACAACAAGTTCTGGAGGACATCCCCTTGAATTTTTACGGAATCAGCCTCAATTTCAACAGATGAGAAAAT
TATTCAACAGAATCCTTCCCTGCTTCCAGCATTGCTACAACGGATAGGTCGGGAAGATCCTCAGTTACTTCAGCAAATTA
GCCAACACCAGGAGCATTTTATACAGATGTTAAATGAACTGGTTCAAGAAGCTGGTGGTCAAGGAGGAGGGGGTGGAGGG
GGCAGTTGAGGAATTGCAGAAGCTGGAAGTGGTCATATGAACTACATTCAAGTAACGCCTCAGGAAAAAGAAGCTATAGA
AAGGCTAAAGGCTTTGGGATTTCCTGAAGGACTTGTGATACAAGCATATTTTGCCTGTGAGAAGAACGAGAACTTGGCTG
CCAAGTTTCTTCTACAGCAAAACTTTCATGAAGAT

Alignment

ORF - retro_ecab_361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVTTPAPATTQQSN
          VKAL.EKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVTTPAPATTQQSN
Retrocopy VKALEEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVVVMVTKPKAVTTPAPATTQQSN

Parental  SATTTTV-SSSTAPAAAQAPTPAPALAPAPTPASITPASTTASSEPAPASATKQEKPAEKPAEAPVATSP
          SAT.TT..SSSTAPA.AQAPTPAPALAP.PTPASITPAS.TASSEPAPASATKQEKPAEKPAE.PVATSP
Retrocopy SAT-TTT>SSSTAPAVAQAPTPAPALAPTPTPASITPASATASSEPAPASATKQEKPAEKPAETPVATSP

Parental  TSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMGIPG
          TSTD.TSGDSSRSNLFEDATSALVTGQSYENMV.EIMSMG.EREQVIAALRASFNNPDRAVEYL.MGIPG
Retrocopy TSTDCTSGDSSRSNLFEDATSALVTGQSYENMVAEIMSMGCEREQVIAALRASFNNPDRAVEYLFMGIPG

Parental  DRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPLEFLRNQPQFQQMR-QIIQQNPSLLPA
          DRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPLEFLRNQPQFQQMR..IIQQNPSLLPA
Retrocopy DRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPLEFLRNQPQFQQMR<KIIQQNPSLLPA

Parental  LLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIAEAGSGHMNYIQVTPQEKEAIE
          LLQ.IGRE.PQLLQQISQHQEHFIQMLNE.VQEAGGQGGGGGGGS.GIAEAGSGHMNYIQVTPQEKEAIE
Retrocopy LLQRIGREDPQLLQQISQHQEHFIQMLNELVQEAGGQGGGGGGGS*GIAEAGSGHMNYIQVTPQEKEAIE

Parental  RLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          RLKALGFPEGLVIQAYFACEKNENLAA.FLLQQNF.ED
Retrocopy RLKALGFPEGLVIQAYFACEKNENLAAKFLLQQNFHED

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	1.12 RPM	21.96 RPM
SRP021940_cerebellum	2.08 RPM	34.48 RPM
SRP021940_embryo	4.91 RPM	63.01 RPM
SRP021940_placental_villous	4.14 RPM	44.07 RPM
SRP021940_synovial_membrane	1.54 RPM	30.42 RPM
SRP021940_testis	1.28 RPM	23.15 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_361 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_361 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_361 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361 ,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,