RetrogeneDB ID: retro_ecab_1002

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:82771271..82772398(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000024539
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ODC1
• Ensembl ID: ENSECAG00000022690
• Aliases: None
• Description: ornithine decarboxylase 1 [Source:HGNC Symbol;Acc:8109]

Sequence

>retro_ecab_1002
ATGATTAAGAAACACCTGAGGTGGTTAAAAGCTCTTCCTCGGGTCACCCCCTTTAACGCAGTCAAATGCAATGATAGCAG
AACCATCGTGAAGACCCTGGCTGACGTCGGGACAGGGTTTGACTGTGCCAGCAAGACTGAAATACAACTGATGCTGAGTC
TCAGGGTGCCTCCAGAGAGAATTATCTGCGCAAATCCTTGTAAACAAGTGTCCCAGGTTAGGTACGCTGCCAATAACGGA
GTCCAAATGATGACTTTTGATAGTGAGGTCGAGTTGATGAAAGTTGCCAGGGCACATCCAAAGGCAGAGTTGGTTTTGCG
GATTGCTACCAATGATTCCAAAGCAGTCCGTCGCCTCAGTGTTAAATTTGGTGCCACACTCAAAACCAGCAGGCTTCTTT
TGGAATGGGCTAAAGAGCTAAATATTGACGTCATTCGTGTCAGCTCCCATGTGGGAAGTGGCTGCACTGACCCGGAGACC
TTTGTGCAGGCCATCTCTGATGCCCGCTGTGTCTTTGATATGGGGGCTGAAATTTGTTTCAGCGTATATCAGCTTGATAT
TGGTGGTGGCTTTCCTGGATCTGAGGAGATAAGGCTTAAATTTGAAGAGGTCACCAGTGTAATCAACCCAGCACCAGACA
AGTATTTTGCGTCAGACTCCGGAGTGAGAGTCATAGCTGAGCCAGGCGGATACTATGTTGCATCAGCTTTCAGGCTCGCA
GTTAATATCATTGCGAAAAAACTCATATTAAAGGAACAAACAGGAGCTGATGATGATGAGTCGAGTGAACAAACCTTTGT
GTATTACGTGAATGATGGAGTATACGGATCATTTCATTGCATCCTTTATGATCATGCACACGTGAAGCCTCTTCTGCAAA
AGAGATCCAAACCAGATAAGTATATTCGTCCAGTATATGGGGACCGACCTGTGACAGCCTTGATTGCATTGTTGAGCGCT
GTAACTTGCCCCAGATGCAGGTGGGCGATTGGATGCTTTTTGAAAACATGGGTGCTTATACTGTTGCTGCTGCTTGTACT
TTCAACGGATTCCAGAGGCCAGCTATCTACTATGTGATGTTGGGGCCAACATGGCTCGACTTCCCACATGAAGTGCAGGA
GCAGGAC

Alignment

ORF - retro_ecab_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 81.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILKKHLRWLKALPRVTPFYAVKCNDSRTIVKTLAAIGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQV
          ..KKHLRWLKALPRVTPF.AVKCNDSRTIVKTLA..GTGFDCASKTEIQL..SL.VPPERII.ANPCKQV
Retrocopy MIKKHLRWLKALPRVTPFNAVKCNDSRTIVKTLADVGTGFDCASKTEIQLMLSLRVPPERIICANPCKQV

Parental  SQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKEL
          SQ..YAANNGVQMMTFDSEVELMKVARAHPKA.LVLRIAT.DSKAV.RLSVKFGATLKTSRLLLE.AKEL
Retrocopy SQVRYAANNGVQMMTFDSEVELMKVARAHPKAELVLRIATNDSKAVRRLSVKFGATLKTSRLLLEWAKEL

Parental  NIDVIGVSFHVGSGCTDPETFVQAISDARCVFDMGAEIGFNMYLLDIGGGFPGSEDVKLKFEEVTSVINP
          NIDVI.VS.HVGSGCTDPETFVQAISDARCVFDMGAEI.F..Y.LDIGGGFPGSE...LKFEEVTSVINP
Retrocopy NIDVIRVSSHVGSGCTDPETFVQAISDARCVFDMGAEICFSVYQLDIGGGFPGSEEIRLKFEEVTSVINP

Parental  ALDKYFPSDSGVRVIAEPGRYYVASAFTLAVNIIAKKLVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFN
          A.DKYF.SDSGVRVIAEPG.YYVASAF.LAVNIIAKKL.LKEQTG.DD.DESSEQTF.YYVNDGVYGSF.
Retrocopy APDKYFASDSGVRVIAEPGGYYVASAFRLAVNIIAKKLILKEQTGADD-DESSEQTFVYYVNDGVYGSFH

Parental  CILYDHAHVKPLLQKRPKPDEKY-YSSSIWGPTCDGLDRIVERCNLPEMQVGDWMLFENMGAYTVAAAST
          CILYDHAHVKPLLQKR.KPD.KY.YSSSIWGPTCD.LD.IVERCNLP.MQVGDWMLFENMGAYTVAAA.T
Retrocopy CILYDHAHVKPLLQKRSKPD-KY<YSSSIWGPTCDSLDCIVERCNLPQMQVGDWMLFENMGAYTVAAACT

Parental  FNGFQRPTIYYVMSGPTW-QLMQQIQNHD
          FNGFQRP.IYYVM.GPTW.......Q..D
Retrocopy FNGFQRPAIYYVMLGPTWLDFPHEVQEQD

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	0.06 RPM	25.26 RPM
SRP021940_cerebellum	0.05 RPM	25.08 RPM
SRP021940_embryo	0.08 RPM	146.81 RPM
SRP021940_placental_villous	0.00 RPM	82.70 RPM
SRP021940_synovial_membrane	0.03 RPM	41.15 RPM
SRP021940_testis	0.06 RPM	260.50 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1002 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1002 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011415	1 retrocopy	retro_amel_414,
Bos taurus	ENSBTAG00000004256	1 retrocopy	retro_btau_552,
Choloepus hoffmanni	ENSCHOG00000010898	2 retrocopies	retro_chof_1618, retro_chof_2111,
Dasypus novemcinctus	ENSDNOG00000018474	31 retrocopies	retro_dnov_1032, retro_dnov_1128, retro_dnov_1129, retro_dnov_1137, retro_dnov_1212, retro_dnov_1235, retro_dnov_1418, retro_dnov_1434, retro_dnov_1493, retro_dnov_1594, retro_dnov_1595, retro_dnov_1677, retro_dnov_1778, retro_dnov_1810, retro_dnov_1813, retro_dnov_2016, retro_dnov_2027, retro_dnov_2108, retro_dnov_2147, retro_dnov_2180, retro_dnov_2212, retro_dnov_2461, retro_dnov_2551, retro_dnov_2564, retro_dnov_392, retro_dnov_740, retro_dnov_766, retro_dnov_781, retro_dnov_923, retro_dnov_943, retro_dnov_958,
Equus caballus	ENSECAG00000016922	1 retrocopy	retro_ecab_1096,
Equus caballus	ENSECAG00000022690	2 retrocopies	retro_ecab_1002 , retro_ecab_957,
Loxodonta africana	ENSLAFG00000005330	2 retrocopies	retro_lafr_218, retro_lafr_850,
Myotis lucifugus	ENSMLUG00000010423	1 retrocopy	retro_mluc_281,
Macaca mulatta	ENSMMUG00000020441	2 retrocopies	retro_mmul_157, retro_mmul_1645,
Monodelphis domestica	ENSMODG00000014779	1 retrocopy	retro_mdom_262,
Ictidomys tridecemlineatus	ENSSTOG00000000386	2 retrocopies	retro_itri_1751, retro_itri_801,
Tursiops truncatus	ENSTTRG00000004611	3 retrocopies	retro_ttru_1940, retro_ttru_731, retro_ttru_843,