RetrogeneDB ID: retro_amel_1140

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192950.1:193398..194230(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000007786
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1LMH6]

Sequence

>retro_amel_1140
AAAACATCACTAAATTTAAGCCAAAATGGAAAAGGAAAAGATTCACATCATACTGCTATCATTGGACATGCAAATTCAAG
CAAGTCTATTACTACTGGCCATCTGTTCTACAAACGTGGTTGGAATCAACAGAATAACCATCAACATTTTTGAGAATGAG
TCTGCTAAAATGGGAAAGTCTCCTTTAGATATGCCTGGATCTTGGAAAAACTTAAAGCTGAGTGTGAATATGGTATCACC
ATGGGCATCTCCTTGTGGAAATTTGAGACCAGTAAAAATATGGTCATCACTAATGCTCCAGGACACAGAGATTTTATCAA
AAATATGATCATGGGTACATCTCAGGCTGACAGTTTTGTTCTGATTGTTGCTGCTGGTATTTGTAAAATTGGAGCTGGTA
TCTCCAAGATCGTGTGGACCTATCAGCATGGTTTATGGCTTACATGTTGGGTTTGAACCAACTAATTGTTGGTGTTAACA
CAGTGGATTCTACTGAGCCACTCTATAGTTAGAAGAGATATGAGGAAGTCAGTTTCCGCATTAAGAAAAGTTTCTATAAA
CTTAACACAGCAGCATTTATGCCAACTTCTGGTTTGAATGGTGGAACATTCTGGAGTTAAGTGCTAAAATACTTTGGTTC
AAGGGATGGAAATTCACTAGAAGGATGGAAGTGCCAGTGGAACTACACCGCTTGAAGCTCTGGATTATATCCTGTCACCA
ACTCATACAATTGACAAGTCCTTCATCTCTCCCTCCAGATCGTTTATAAAACTGGTGGTATTAGTATAGCTGCTGTGAGC
TGAGCAGAAACTAGTGCTCTAAACCAGGCATA

Alignment

ORF - retro_amel_1140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.54 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KPPLNLNQNGKGKDSH-IVVIGHVDSGKSTTTGHLIYKCG-GIDKRTIEKFEKEAAEMGKG-SFKYAWVL
          K..LNL.QNGKGKDSH....IGH..S.KS.TTGHL.YK.G.GI...TI..FE.E.A.MGK..SF.YAW.L
Retrocopy KTSLNLSQNGKGKDSHHTAIIGHANSSKSITTGHLFYKRG>GINRITINIFENESAKMGKS<SFRYAWIL

Parental  DKLKAERERGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKN
          .KLKAE.E.GIT..ISLWKFETSK..V.I..APGHRDFIKNMI.GTSQAD..VLIVAAG.....AGISK.
Retrocopy EKLKAECEYGITMGISLWKFETSKNMV-ITNAPGHRDFIKNMIMGTSQADSFVLIVAAGICKIGAGISKI

Parental  GQTREYAL-LAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGD
          ..T....L..AY.LG..QLIVGVN..DSTEP.YS.KRYEE.....S..IKK..Y...T.AF.P.SG.NG.
Retrocopy VWTYQHGL<MAYMLGLNQLIVGVNTVDSTEPLYS*KRYEEV----SFRIKKSFYKLNTAAFMPTSGLNGG

Parental  -NMLEPSANMPWFKGWKVTR-KDGNASGTTLLEALDCILPPTRPTDKP-LRLPLQDVYKIGGIGTVPVGR
          .N.LE.SA...WFKGWK.TR.KDG.ASGTT.LEALD.IL.PT...DK..L.L.LQ.VYK.GGI....V..
Retrocopy <NILELSAKILWFKGWKFTR<KDGSASGTTPLEALDYILSPTHTIDKS<LHLSLQIVYKTGGISIAAVS*

Parental  VETGVL-KPGM
          .ET..L.KPG.
Retrocopy AETSAL<KPGI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1140 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1140 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007786	14 retrocopies	retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140 , retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,