RetrogeneDB ID: retro_ecab_865

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:72674387..72675756(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015105
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LPCAT2
• Ensembl ID: ENSECAG00000009649
• Aliases: None
• Description: lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]

Sequence

>retro_ecab_865
ATCATCCTCACCGGGAGTGTGCTGGTGCCCGTTCGGGTGTCCTGCATCGCCTTCCTCTTCATCTTCCTCTGGCCAGTGGC
CATACTTTCCACCGTGGGCCTTTCGGCTCAACCAACCAAGCCCGCTAAGAGTTGGAGAAGAACACTAATGCAGTCAGCCC
TCAAGTTCTTGTTTCAGGCGACGTTCTTTTTAGCAGGGTTCCTGGTTAAAGTGAAAGGGAAAAAGGCAACCCGAGACGAG
GCCCCCATCTTCGTGACAGCGCCGCACTCTACTTTCTTTGACGCTATCGCCTGTGTGGTGGCAGGGTTACCCTCAGTGGT
CTCCGCAAGTCAAAACGCGCTGATCCCTGTGGCTGGGAAACTCCTACTGTCAACACAGCCCGTGCTTGTGACGCGAGAGG
ACCCAAATTCCAGGAAGAATACCAAGAATGAAATCCTGAGGCGAGTGACATCTGAAAGGAAGTGGCCACAGATCCTCATT
TTCCCGGAAGGAGTGTGTACCAATCGCACGTGTCTGGTCACCTTTAAACTAGGAGCCTTCTCTCCAGGTGTTCCTGTGCA
GCCAGTGCTGCTCAGGTACCCAAACACGCTGGACACGGTGACCTGGACCTGGCAGGGTTTCACAGGCTTCCAGGCCTGTA
TGCTGACCCTGAGTCAACTCTTCACCAGGGTAGAAGTGGAGTTTATGCCTGTTTATATCCCAAATGACCAAGAAAAAAAA
GACCCGGTCCTTTTTGCCAATACAGTGAGGATCAACATGGCAAATGCTCTGGGGGTGCCTGTGACAGACCACACTTATGA
AGACTGCAGACTGATGATTTCCACAGGTAACCTTCAACTACCCACGGAAGCTGGTTTGGTGGGATTTACAAAAATTAGCC
AGAAATTGAAGTTAGATTGGGATAATATTCATCAGCATTTGGATGAATATGCTGCAATTGCAGTTGCCTCAAAAGGAGGG
AAGATAGAAATTGAAGTTTGCAAATTATTTAAAACTCCCAATTTAAGAGCCCTTGAGACAACTTTTTGCCCTCTTTGACA
GGAATAATGAGGGCAGCATAGACCTCAGAGAGTATGTGATAGGTCTGACTGTCCTATGCAATTCCGCCAACACTGAAAAG
ATTCTGCAAATGTCATTTAAGTTTTTTGATCTTGATGAGCATGGTTTTATAACAAAACAGGAGTTAGCTGCTACACTTTG
GACAGCTTTTGGAGTGCCAGATCTTGACGTTTCCAGACTCTTTCAGGAAATAGCTGGACAGAGCTCAGAGTCCATTTCAT
ACGAGAAGTTTAAGAAATTTGCCCTGAGGCATCCACAATATGCCAAGTTATTTAATTCATACTTAGATCTTCAGGCAGCC
TATATATAT

Alignment

ORF - retro_ecab_865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.1 %
• Parental protein coverage: 93.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFFLGIILLPIRALLVALILLLAWPFAAISTACCPEKLTHPVTGWRRKITQPVLKFLGRALFFSMGFIVT
          I...G..L.P.R....A......WP.A..ST.......T.P...WRR...Q..LKFL..A.FF..GF.V.
Retrocopy IILTGSVLVPVRVSCIAFLFIFLWPVAILSTVGLSAQPTKPAKSWRRTLMQSALKFLFQATFFLAGFLVK

Parental  VKGKVANAVEAPIFVVAPHSTFFDGIACVIAGLPSMVSRNENAQAPLVGRLLRALQPVLVSRVDPDSRKN
          VKGK.A...EAPIFV.APHSTFFD.IACV.AGLPS.VS...NA..P..G.LL...QPVLV.R.DP.SRKN
Retrocopy VKGKKATRDEAPIFVTAPHSTFFDAIACVVAGLPSVVSASQNALIPVAGKLLLSTQPVLVTREDPNSRKN

Parental  TINEIIRRATSGGEWPQMLVFPEGTCTNRSCLITFKPGAFIPGVPVQPILLRYPNKLDTVTWTWQGYTFI
          T.NEI.RR.TS...WPQ.L.FPEG.CTNR.CL.TFK.GAF.PGVPVQP.LLRYPN.LDTVTWTWQG.T..
Retrocopy TKNEILRRVTSERKWPQILIFPEGVCTNRTCLVTFKLGAFSPGVPVQPVLLRYPNTLDTVTWTWQGFTGF

Parental  QLCMLTFCQPFTRVEVEFMPVQVPNEEERNDPVLFADRVRNLMAQALGIPVTDHTYEDCRLMISAGQLTL
          Q.CMLT..Q.FTRVEVEFMPV..PN.....DPVLFA..VR..MA.ALG.PVTDHTYEDCRLMIS.G.L.L
Retrocopy QACMLTLSQLFTRVEVEFMPVYIPNDQXXXDPVLFANTVRINMANALGVPVTDHTYEDCRLMISTGNLQL

Parental  PMEAGLVEFTKISRKLKLDWDGIRKHLDEYATIASSSKGGRIGIEEFAEYLKLP-VSDVLRQLFALFDRN
          P.EAGLV.FTKIS.KLKLDWD.I..HLDEYA.IA..SKGG.I.I.E.....K.P.....LRQLFALFDRN
Retrocopy PTEAGLVGFTKISQKLKLDWDNIHQHLDEYAAIAVASKGGKIEI-EVCKLFKTP>I*EPLRQLFALFDRN

Parental  HDGSIDFREYVIGLAVLCNPANTEEIIQVAFKLFDVDEDGHITEEEFSTILQASLGVPDLDVSGLFKEIA
          ..GSID.REYVIGL.VLCN.ANTE.I.Q..FK.FD.DE.G.IT..E....L....GVPDLDVS.LF.EIA
Retrocopy NEGSIDLREYVIGLTVLCNSANTEKILQMSFKFFDLDEHGFITKQELAATLWTAFGVPDLDVSRLFQEIA

Parental  --QGDSVSYEEFKSFALKHPEYAKIFTTYLDLQTSHVF
          .....S.SYE.FK.FAL.HP.YAK.F..YLDLQ.....
Retrocopy GQSSESISYEKFKKFALRHPQYAKLFNSYLDLQAAYIY

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	0.06 RPM
SRP021940_cerebellum	0.00 RPM	2.34 RPM
SRP021940_embryo	0.05 RPM	3.40 RPM
SRP021940_placental_villous	0.05 RPM	3.13 RPM
SRP021940_synovial_membrane	0.00 RPM	1.65 RPM
SRP021940_testis	53.20 RPM	3.84 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_865 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_865 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_64
Mus musculus	retro_mmus_270
Rattus norvegicus	retro_rnor_309

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019272	1 retrocopy	retro_btau_64,
Callithrix jacchus	ENSCJAG00000012902	1 retrocopy	retro_cjac_2945,
Dasypus novemcinctus	ENSDNOG00000006859	1 retrocopy	retro_dnov_1735,
Dipodomys ordii	ENSDORG00000013193	1 retrocopy	retro_dord_399,
Equus caballus	ENSECAG00000009649	1 retrocopy	retro_ecab_865 ,
Erinaceus europaeus	ENSEEUG00000014277	1 retrocopy	retro_eeur_109,
Homo sapiens	ENSG00000087253	1 retrocopy	retro_hsap_185,
Gorilla gorilla	ENSGGOG00000005144	1 retrocopy	retro_ggor_266,
Loxodonta africana	ENSLAFG00000003965	1 retrocopy	retro_lafr_66,
Myotis lucifugus	ENSMLUG00000004008	1 retrocopy	retro_mluc_88,
Macaca mulatta	ENSMMUG00000004478	1 retrocopy	retro_mmul_392,
Mus musculus	ENSMUSG00000033192	1 retrocopy	retro_mmus_270,
Nomascus leucogenys	ENSNLEG00000001258	1 retrocopy	retro_nleu_994,
Pongo abelii	ENSPPYG00000007358	1 retrocopy	retro_pabe_445,
Pan troglodytes	ENSPTRG00000008124	2 retrocopies	retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus	ENSPVAG00000007801	1 retrocopy	retro_pvam_173,
Rattus norvegicus	ENSRNOG00000016643	1 retrocopy	retro_rnor_309,
Sorex araneus	ENSSARG00000011914	1 retrocopy	retro_sara_88,
Sarcophilus harrisii	ENSSHAG00000012383	1 retrocopy	retro_shar_116,
Tursiops truncatus	ENSTTRG00000001182	1 retrocopy	retro_ttru_188,