RetrogeneDB ID: retro_ecab_1082

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:75023094..75023661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSECAG00000022692
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_ecab_1082
AAAATGTTCATCGGGGGCCTCTCCGGGAATGTCAGTAAGCAAGGCCTTCTTGACTACCTCAGCCAGTTTGGCGAGGTCGT
AGATTTCATTATTAAAATCCACCCAGGCACTGGCCTATCCAGGGGGTTTGGATTTGTGCTTTTCAAAGATAGTGCCACTG
TTGAAAAGGTGCTCCAAGTCAAAGAGCACAAACTGGATGGCAAGACGATCCAGCTTAGAAGGGCTAAAGCCGTAGTATCG
AGATTCCCTCCCAAAAAGGTTTTTGTGGGAGGGCTGAACCCTCGTCTGTCTGAAGAAAAAATCAGACAGTACTTTGGGAC
GTTCGGAGTGATTCAGGATATCAAGCTTCCAGTGAATTCCAAAACAAATGAAAGACGAGCTTTCTGTTTTATCACGTATG
CTGATGAAAAGGCAGTGAGGAAGCTGTTAGAAACCAGGTACCATCGAATTGGCTCCAGGCGGTGTGAAGTTAAAATCGCA
TTCCCAAAGGAATATAAGAGGCTGCGACAGCTGGGAGGAAGAGATGCTCCGTTTGCCAGGCTGAGCAGCTCCCGGGATGG
AAGAGGC

Alignment

ORF - retro_ecab_1082 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 70.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLI
          KMFIGGLS...SK..L..YLS.FGEVVD..IK..P.TG.SRGFGFVLFKD.A.V.KVL..KEHKLDGK.I
Retrocopy KMFIGGLSGNVSKQGLLDYLSQFGEVVDFIIKIHPGTGLSRGFGFVLFKDSATVEKVLQVKEHKLDGKTI

Parental  DPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVK
          ...RAKA.....PPKKVFVGGL.P..SEE.I..YFG.FG.I..I.LP...KTNERR.FCFITY.DE..V.
Retrocopy QLRRAKAVVSRFPPKKVFVGGLNPRLSEEKIRQYFGTFGVIQDIKLPVNSKTNERRAFCFITYADEKAVR

Parental  KLLESRYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTR-GRG
          KLLE.RYH.IGS..CE.K.A.PKE..R..Q....GGR.A........R.GRG
Retrocopy KLLETRYHRIGSRRCEVKIAFPKEYKRLRQ---LGGRDAPFARLSSSRDGRG

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	0.00 RPM	57.14 RPM
SRP021940_cerebellum	0.00 RPM	83.77 RPM
SRP021940_embryo	0.00 RPM	218.14 RPM
SRP021940_placental_villous	0.00 RPM	77.80 RPM
SRP021940_synovial_membrane	0.00 RPM	43.95 RPM
SRP021940_testis	1.79 RPM	54.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1082 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1082 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Equus caballus	ENSECAG00000008676	1 retrocopy	retro_ecab_74,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082 ,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,